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| Status |
Public on May 05, 2024 |
| Title |
tracheal aspirate, NoDex, patient 24, scRNAseq |
| Sample type |
SRA |
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| Source name |
tracheal aspirate
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| Organism |
Homo sapiens |
| Characteristics |
disease: COVID-19
tissue: tracheal aspirate
study days: 0
treatment: NoDex
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| Treatment protocol |
The Dex group received at least one dose of 6mg dexamethasone at the time of initial biosampling
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| Extracted molecule |
total RNA |
| Extraction protocol |
The tracheal aspirate (TA) samples were transported to a BSL-3 laboratory, 3 mL of TA was dissociated using 50 µg/mL collagenase type 4 (Worthington), and 0.56 ku/mL of Dnase I (Worthington). The single-cells were collected by centrifugation and counted, and the CD45-positive cells were enriched using MojoSort Human CD45 beads (Biolgenend) and counted again before library preparation. For the whole-blood (WB) samples, the peripheral blood was collected into EDTA tubes (BD, 366643). 500 μl of peripheral blood was treated with RBC lysis buffer (Roche, 11-814-389-001) according to the manufacturer’s instructions and the single cells were collected and counted.
For both TA and WB samples, the Chromium Controller was loaded with 15,000 cells per sample following the manufacturer’s instructions (10X Genomics). Some samples were pooled together (at 15,000 cells per sample) before GEM partitioning. A Chromium Single Cell 5′ Reagent Kit v2 (10X Genomics) was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries (following the detailed protocol provided by 10X Genomics). Libraries were sequenced on an Illumina NovaSeq6000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The BCL files from sequencer were demultiplexed into individual libraries using mkfastqs command in Cellranger 3.0.1 suite of tools (https://support.10xgenomics.com).
The feature-barcode matrices were obtained for each library by aligning the WB raw fastq files to GRCh38 reference genome (annotated with Ensembl v85) and TA raw fastq files to GRCh38 (annotated with Ensembl v85) + SARS-CoV-2 reference genome using default parameters in Cellranger count (v3.0.1).
Assembly: GRCh38 (WB); GRCh38 + SARS-CoV-2 reference genome (TA)
Supplementary files format and content: The count matrices from cellranger are provided as H5 files, the Hierarchical Data Format, that is exported by cellranger-count.
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| Submission date |
Jun 28, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Ravi Patel |
| E-mail(s) |
ravi.patel2@ucsf.edu
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| Organization name |
University of California San Francisco
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| Department |
CoLabs
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| Lab |
Fragiadakis lab
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| Street address |
513 Parnassus Ave
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE236030 |
Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19 |
| GSE237180 |
Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19. |
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| Relations |
| BioSample |
SAMN36025621 |
| SRA |
SRX20811755 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7517090_MVIR1-HS24-D0ETA1-SCG1_raw_feature_bc_matrix.h5 |
19.4 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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